Effects of synonymous mutations on kinetic properties and structure of firefly luciferase: Molecular dynamics simulation, molecular docking, RNA folding, and experimental study

• Published in: International journal of biological macromolecules Vol. 235; p. 123835
• Main Authors: Mortazavi, Mojtaba, Torkzadeh-Mahani, Masoud, Rahimi, Mehdi, Maleki, Mahmood, Lotfi, Safa, Riahi-Madvar, Ali
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.04.2023
• Subjects: Homology modeling; Luciferases, Firefly - metabolism; Molecular docking; Molecular Docking Simulation; Molecular Dynamics Simulation; Molecular dynamics simulations; Rare codon; RNA Folding; Silent Mutation; Thermal stability; Rare codon; RNA folding; Molecular dynamics simulations; Thermal stability; Molecular docking; Homology modeling
• ISSN: 0141-8130; 1879-0003
• DOI: 10.1016/j.ijbiomac.2023.123835

Although synonymous mutations have long been thought to lack striking results, a growing body of research shows these mutations have highly variable effects. In this study, the impact of synonymous mutations in the development of thermostable luciferase was investigated using a combination of experimental and theoretical approaches. Using bioinformatics analysis, the codon usage features in the Lampyridae family's luciferases were studied and four synonymous mutations of Arg in luciferase were created. An exciting result was that the analysis of kinetic parameters showed a slight increase in the thermal stability of the mutant luciferase. AutoDock Vina, %MinMax algorithm, and UNAFold Server were used to perform molecular docking, folding rate, and RNA folding, respectively. Here, it was assumed that in the region (Arg337) with a moderate propensity for coil, synonymous mutation altered the rate of translation, which in turn may lead to a slight change in the structure of the enzyme. According to the molecular dynamics simulation data, local minor global flexibility is observed in the context of the protein conformation. A plausible explanation is that this flexibility may strengthen hydrophobic interactions due to its sensitivity to a molecular collision. Accordingly, thermostability originated mainly from hydrophobic interaction.